parseacd.java

emboss的linux版本的源代码

    while((stop = help.indexOf(' ',55))>0)
    {
      helpText = helpText.concat(help.substring(start,stop) + "\n");   
      help = help.substring(stop+1,help.length());
    }
    helpText = helpText.concat(help);

    return helpText;
  }


  /**
  *
  * Determine if there is a optional parameter in a field of the ACD.
  * @param field 	field number
  * @return  		true if this is an "optional" field.
  *
  */
  public boolean isOptionalParamValue(int field) 
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
    {
      if(getParameterAttribute(field,i).startsWith("opt")) 
        return true;
    }
    return false;
  }


  /**
  *
  * Determine if data type of a field is seqout.
  * @param field 	field number
  * @return  		true if this is an "seqout" field.
  *
  */
  public boolean isOutputSequence(int field) 
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("seqout"))
          return true;
    }
    return false;
  }


  /**
  *
  * Gets the name of the output sequence field (seqout).
  * @param field	field number
  * @return  		parameter name for the seqout data type.
  *
  */
  public String getOutputSequenceFile(int field) 
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
      if (getParameterAttribute(field,i).startsWith("seqout")) 
          return getParamValueStr(field,i);
    return "";
  }


  /**
  *
  * Determine if a field is data type graph or xygraph.
  * @param field	field number
  * @return 		true if the field is of "graph" or 
  *			"xygraph" type.
  *
  */
  public boolean isOutputGraph(int field) 
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
    {
      if ( getParameterAttribute(field,i).startsWith("graph") ||
           getParameterAttribute(field,i).startsWith("xygraph") )
          return true;
    }
    return false;
  }


  /**
  *
  * Determine if a field is data type outfile.
  * @param field	field number
  * @return  		true if the field is of "outfile" type.
  *
  */
  public boolean isOutputFile(int field)   
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("outfile"))
          return true;
    }
    return false;
  }


  /**
  *
  * Gets a String default parameter.
  * @param field	field number
  * @return 		default parameter for this field.
  *
  */
  public String getDefaultParamValueStr(int field) 
  {
    int num = getNumofParams(field);

    ApplicationFields aF = (ApplicationFields)vappF.get(field);
    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("def")) 
        return aF.getParamValueStr(i);
    }
    return "";
  }


  /**
  *
  * Used for a list data type to put the list items in a String array.
  * @param field	field number
  * @return		String array representation of the list type.
  *
  */
  public String[] getList(int field) 
  {
    int num = getNumofParams(field);

    String delim     = ";";  // list item delimeter default
    String codedelim = ":";  // label delimeter default
    String listAll = null;
    String list[];
    String item;
  
    ApplicationFields aF = (ApplicationFields)vappF.get(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("val")) 
        listAll = aF.getParamValueStr(i);
      if (getParameterAttribute(field,i).startsWith("delim")) 
        delim = aF.getParamValueStr(i);
      if (getParameterAttribute(field,i).startsWith("codedelim"))
        codedelim = aF.getParamValueStr(i);

    }

    if(delim == null || listAll == null)
       System.out.println("getList ERROR");

    StringTokenizer st = new StringTokenizer(listAll,delim);

    int n = 0;
    while (st.hasMoreTokens()) 
    {
      st.nextToken(delim);
      n++;
    }

    list = new String[n];
    
    st = new StringTokenizer(listAll);
    n = 0;

    boolean ldef = false;
    Vector def = new Vector();

    //put the default values into a vector
    if(isDefaultParamValueStr(field))
    {
      ldef = true;
      String sdef = getDefaultParamValueStr(field);
      StringTokenizer stdef = new StringTokenizer(sdef);
      while(stdef.hasMoreTokens())
        def.add(stdef.nextToken(delim));
    }
     
    listdefault = new Vector();  
    while (st.hasMoreTokens()) 
    {
      String key = st.nextToken(codedelim);
      item = st.nextToken(delim);

      if(ldef)
      {
        int newline = key.indexOf("\n");
        if(newline > -1)
          key = key.substring(newline+1,key.length());
        newline = key.indexOf(delim);
        if(newline > -1)
          key = key.substring(newline+1,key.length());

        key = key.trim();

        // check if it is a default value
        for(int i=0;i<def.size();i++)
          if(key.equals((String)def.get(i)))
            listdefault.add(new Integer(n));
      }
      item = item.substring(1,item.length()).trim();
      list[n] = new String(item); 
      n++;
    }

    return list;
  }


  /**
  *
  * For a list data type determine the appropriate String entry.
  * @param field	field number
  * @param index	index into the list
  * @return 		String for that entry.
  *
  */
  public String getListLabel(int field, int index) 
  {
    int num = getNumofParams(field);

    String delim     = ";";  // list item delimeter default
    String codedelim = ":";  // label delimeter default
    String listAll = null;
    String item;
    String key="";

    ApplicationFields aF = (ApplicationFields)vappF.get(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("val"))
        listAll = aF.getParamValueStr(i);
      if (getParameterAttribute(field,i).startsWith("delim"))
        delim = aF.getParamValueStr(i);
      if (getParameterAttribute(field,i).startsWith("codedelim"))
        codedelim = aF.getParamValueStr(i);
    }

    if(delim == null || listAll == null)
       System.out.println("getList ERROR");

    StringTokenizer st = new StringTokenizer(listAll,delim);

    st = new StringTokenizer(listAll);

    for(int i=0;i<index+1;i++) 
    {
      key = st.nextToken(codedelim);
      item = st.nextToken(delim);
    }
    if(index>0)
      key = key.substring(1,key.length()).trim();
    else
      key = key.substring(0,key.length()).trim();

    return key;

  }


  /**
  *
  * Used for a selection type to put the list items in a String array.
  * @param field	field number
  * @return 		String array representation of the select type.
  *
  */
  public String[] getSelect(int field) 
  {
    int num = getNumofParams(field);

    String delim     = ";";  // select item delimeter default
    String listAll = null;
    String list[];
    String item;

    ApplicationFields aF = (ApplicationFields)vappF.get(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("val"))
        listAll = aF.getParamValueStr(i);
      if (getParameterAttribute(field,i).startsWith("delim"))
        delim = aF.getParamValueStr(i);
    }

    if(delim == null || listAll == null)
       System.out.println("getSelect ERROR");

    StringTokenizer st = new StringTokenizer(listAll,delim);

    int n = 0;
    while (st.hasMoreTokens()) 
    {
      st.nextToken(delim);
      n++;
    }

    list = new String[n];
   
    boolean ldef = false;
    Vector def = new Vector();
    //put the default values into a vector
    if(isDefaultParamValueStr(field))
    {
      ldef = true;
      String sdef = getDefaultParamValueStr(field);
      StringTokenizer stdef = new StringTokenizer(sdef);
      while(stdef.hasMoreTokens())
        def.add(stdef.nextToken(delim).trim());
    }

    st = new StringTokenizer(listAll);
    n = 0;
    listdefault = new Vector();

    while (st.hasMoreTokens()) 
    {
      item = st.nextToken(delim);
      if(ldef)
      {
//      if (item.endsWith(getDefaultParamValueStr(field)))
//        listdefault.add(new Integer(n));

        for(int i=0;i<def.size();i++)
          if( item.equals((String)def.get(i)) ||
              Integer.toString(n+1).equals((String)def.get(i)) )
            listdefault.add(new Integer(n));
      }

      item = item.substring(0,item.length()).trim();
      list[n] = new String(item);
      n++;
    }

    return list;
  }


  /**
  *
  * Use this after getList or getSelect to retrieve default
  * @return 	default for list or select data type
  *
  */
  public Vector getListOrSelectDefault()
  {
    return listdefault;
  }


  /**
  *
  * Determine if there is a optional parameter in any field of the ACD.
  * @param 	true if there is an optional parameter in any field.
  *
  */
  public boolean isOptionalParam()
  {
    for(int i=0;i<numofFields;i++)
      if(isOptionalParamValue(i)) return true; 
    
    return false;
  }

  /**
  *
  * Gets the number of fields in the ACD file.
  * @return  	total number of fields in an ACD file
  *
  */
  public int getNumofFields() 
  {
    return numofFields;
  }


  /**
  *
  * Gets the number of parameters in a ACD field.
  * @param field	field number
  * @return 		number of parameters in the field.
  *
  */ 
  public int getNumofParams(int field) 
  {
    ApplicationFields aF = (ApplicationFields)vappF.get(field);
    return aF.getNumberOfParam();
  }


  /**
  *
  * Parses a parameter in a ACD field 
  * @param in	BufferedReader 
  * @param st	tokenizer
  * @return 	string tokenizer type or zero
  *
  */
  public int parseParam(BufferedReader in, StreamTokenizer st) throws IOException 
  {
 
    char c;
    svalue = null;   
    st.eolIsSignificant(false);
   
// the following are not token delimeters
    st.wordChars((int)'-',(int)'-'); st.wordChars((int)'$',(int)'$');
    st.wordChars((int)'(',(int)'('); st.wordChars((int)')',(int)')');
    st.wordChars((int)'@',(int)'@'); st.wordChars((int)'?',(int)'?');
    st.wordChars((int)'!',(int)'!'); st.wordChars((int)'#', (int)'#');
// the following are token delimeters
    st.whitespaceChars((int)'\n',(int)'\n');
    st.whitespaceChars((int)' ',(int)' ');
    st.whitespaceChars((int)':',(int)':');
    st.whitespaceChars((int)'=',(int)'=');
    st.ordinaryChars((int)'\"', (int)'\"');
    st.ordinaryChars((int)'\'',(int)'\'');

    st.nextToken();
    attr = st.sval;
    if(attr == null) return 0;

//skip commented lines
    if(attr.startsWith("#")) 
    {
      while( (c = (char)in.read()) != '\n') {}
      st.nextToken();
      attr = st.sval;
    }
    if(attr == null) return 0;
 
    st.nextToken();
    svalue = st.sval;
    nvalue = st.nval;
 
   // cope with double quotes by forwarding to end quote
   // and remove unwanted white space
    if( svalue == null &&
        st.ttype != java.io.StreamTokenizer.TT_NUMBER ) 
    {
      svalue = "";
      char last = ' ';
      while( (c = (char)in.read()) != '\"') 
      {
        if( c != ' ' || last != ' ')
          svalue = svalue.concat(java.lang.String.valueOf(c));
        last = c;
      }
    }
 
    numofParams++;
    return st.ttype;
  }


  public int getNumMultiTextField()
  {
    return nmultiTextField;
  }
  
}